I disagree with the premise of your question. I think the overlap is larger than it looks like on the surface. I have come to believe that you cannot do solid secure protocol design without a firm grasp of the basics of encryption schemes. You don't need to be a full fledged cryptographer, but to quote Phil Rogaway, "Reading [Schneier] does not qualify one to do cryptographic design." [1]. In fact, the context in which he wrote "Problems with Proposed IP Cryptography"[1] is a perfect evidence of this: IETF committee designing IPsec, back in 1995, which I think is fair to think of as mostly "professional software developers", was clearly warned about potential consequences of some of their design choices[2] (like using Encrypt-then-MAC), but they reacted quite harshly to his comments and did not take them as seriously as they should have, and actual attacks were demonstrated on those issues years later[3]. For me, reading the mailing list is enough evidence that it is very dangerous to draw the line between secure protocol design and other things. Similarly, I believe the lack of understanding of the reasons behind design choices in a protocol specification will surface as implementation bugs done by purely "secure software development" experts (e.g. "optimization" of random data generation at the beginning of the protocol to use in place of an invalid input by reordering the operations leading to a timing attack in TLS). There is enough historical evidence that makes anything except the "ideal" case dangerous.
[1]: http://www.cs.ucdavis.edu/~rogaway/papers/draft-rogaway-ipse...
[2]: http://www.sandelman.ottawa.on.ca/ipsec/1995/04/msg00148.htm...
[3]: http://www.isg.rhul.ac.uk/~kp/CCSIPsecfinal.pdf
